RetrogeneDB ID:

retro_btau_1830

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:X:80989753..80990731(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KPNA2
Ensembl ID:ENSBTAG00000012225
Aliases:None
Description:importin subunit alpha-2 [Source:RefSeq peptide;Acc:NP_001029621]


Retrocopy-Parental alignment summary:






>retro_btau_1830
GGTGCAGTTGATCCGCTATTGGCACTTCTGGTTGTCCCTGATATGTCATCTCTAGTATGTGGTTACTTACGCAGTCTTAC
CTGGACACTTTCAAATCTTTGTCCCAACAAGAATCCTGCACCCCTCTTAGAGGCTATTGAGCAGATTCTTCCTACTTTAA
TTCATCTCCTACATCACGATGATCCAGAAGTATTAGCTGATACCTGCTGGGCTATTTCCTACCTTACTGGTGGTCCAAAT
GAATGGATTGAAATGATTGTGAAAACTGGGGTTGTACCCCAACTTGTGAAGCTTTTAGGAGCTACTGAATTGCCAGTTGT
GACTCCTGTGCTCAGAGCCACAGGAAATATTGTCACTGGGACACATGAACAAACACAGGTTGTAATAGATGCAGGAGCAC
TTGCTGTATTTCCCAGCCTGCTGACAAACTCCAAAACTAATATTCAGAAGGAAGCTACGTGGACAATGTCAAACATCTCA
GCTGGCCGCCAGCACCAGATACAACAAGTTGTGAATCATGGATTAGTCCCATTCCTTGTTGGCCTTCTCTCAAAGACAGA
CTTTAAGACATAAAAGGAAGCCACATGGGCTGTGAATAACTATACAAGTGGAGGAACTGTTGAGCAGATCGTGTACCTTG
TTCATTGTGGCATAATAGAGCTGTTGATGAACCTCCTAACTGCAAAAGATACCAAAATTGGTCTGGTTATTCTGGATGCC
ATTTCAAATATCTTTTGGGCTGCTGAGAAACTAGGTGAAACTGAGAAACTTAGTATAATGATTGAAGAATGTAGAGGTTT
GGACAAAATTGAAGCTCTACAAAACCATGAAAATGAGTCTGTGTACAAAGCTTCATTAAACTTAATCGAGAAGTATTTCT
TTGTAGAGGAAGAGGAAGATCAAAATGTTGTGCCAGAAACTACCTCTGAAGGCTATACATTCCAAGTGCAGGATGGCTCT
GCTGGGACCTTCAACTTT

ORF - retro_btau_1830 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.41 %
Parental protein coverage: 61.63 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPLEAIEQILPTLVRLLHHDDPEVLADTCW
GAVDPLLALL.VPDMSSL.CGYLR.LTWTLSNLC.NKNPAP.LEAIEQILPTL..LLHHDDPEVLADTCW
RetrocopyGAVDPLLALLVVPDMSSLVCGYLRSLTWTLSNLCPNKNPAPLLEAIEQILPTLIHLLHHDDPEVLADTCW
ParentalAISYLTDGPNERIEMVVKTGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSL
AISYLT.GPNE.IEM.VKTGVVPQLVKLLGATELP.VTP.LRA.GNIVTGT.EQTQVVIDAGALAVFPSL
RetrocopyAISYLTGGPNEWIEMIVKTGVVPQLVKLLGATELPVVTPVLRATGNIVTGTHEQTQVVIDAGALAVFPSL
ParentalLTNSKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGLLSKADFKTQKEAAWAVNNYTSGGTVEQI
LTNSKTNIQKEATWTMSNI.AGRQ.QIQQVVNHGLVPFLVGLLSK.DFKT.KEA.WAVNNYTSGGTVEQI
RetrocopyLTNSKTNIQKEATWTMSNISAGRQHQIQQVVNHGLVPFLVGLLSKTDFKT*KEATWAVNNYTSGGTVEQI
ParentalVYLVHCGIIEPLMNLLTAKDTKIVLVILDAVSNIFRAAEKLGETEKLGIMIEECGGLDKIEALQNHENES
VYLVHCGIIE.LMNLLTAKDTKI.LVILDA.SNIF.AAEKLGETEKL.IMIEEC.GLDKIEALQNHENES
RetrocopyVYLVHCGIIELLMNLLTAKDTKIGLVILDAISNIFWAAEKLGETEKLSIMIEECRGLDKIEALQNHENES
ParentalVYKASLNLIEKYFSVEEEEDQNVVPETTSEGYTFRVQDGSAGTFSF
VYKASLNLIEKYF.VEEEEDQNVVPETTSEGYTF.VQDGSAGTF.F
RetrocopyVYKASLNLIEKYFFVEEEEDQNVVPETTSEGYTFQVQDGSAGTFNF

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
ERP005899_liver 0 .00 RPM 10 .89 RPM
ERP005899_muscle 0 .00 RPM 56 .96 RPM
SRP017611_brain 0 .14 RPM 19 .41 RPM
SRP017611_kidney 0 .12 RPM 26 .02 RPM
SRP017611_liver 0 .00 RPM 12 .46 RPM
SRP030211_testis 0 .27 RPM 438 .79 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_1830 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1830 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1830 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184113 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus ENSBTAG000000048501 retrocopy
retro_btau_1842,
Bos taurus ENSBTAG00000012225 1 retrocopy
retro_btau_1830 ,
Canis familiaris ENSCAFG000000115982 retrocopies
retro_cfam_648, retro_cfam_90,
Cavia porcellus ENSCPOG000000263181 retrocopy
retro_cpor_46,
Dasypus novemcinctus ENSDNOG000000191516 retrocopies
retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus ENSECAG000000205732 retrocopies
retro_ecab_1017, retro_ecab_1123,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG000000019362 retrocopies
retro_fcat_1176, retro_fcat_921,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Oryctolagus cuniculus ENSOCUG000000159134 retrocopies
retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Rattus norvegicus ENSRNOG000000153291 retrocopy
retro_rnor_42,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,


Copyright © RetrogeneDB 2014-2017